rs2159128

Variant names:

• chr19-950380-G-T
• rs2159128
• NM_005224.3:c.694-9712G>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_005224.3(ARID3A):​c.694-9712G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.022 (187 hom., cov: 0)
• Consequence: ARID3A NM_005224.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.758
• Publications: 7 publications found

Genes affected

ARID3A (HGNC:3031): (AT-rich interaction domain 3A) This gene encodes a member of the ARID (AT-rich interaction domain) family of DNA binding proteins. It was found by homology to the Drosophila dead ringer gene, which is important for normal embryogenesis. Other ARID family members have roles in embryonic patterning, cell lineage gene regulation, cell cycle control, transcriptional regulation, and possibly in chromatin structure modification. [provided by RefSeq, Jul 2008]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.118 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ARID3A	NM_005224.3	c.694-9712G>T		intron_variant	Intron 3 of 8	ENST00000263620.8	NP_005215.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ARID3A	ENST00000263620.8	c.694-9712G>T		intron_variant	Intron 3 of 8	1	NM_005224.3	ENSP00000263620.2
ARID3A	ENST00000587532.5	c.235-9712G>T		intron_variant	Intron 1 of 5	5		ENSP00000464969.3
ARID3A	ENST00000457152.3	n.178-9712G>T		intron_variant	Intron 1 of 3	5		ENSP00000440911.2

Frequencies

GnomAD3 genomes AF: 0.0224 AC: 859 AN: 38396 Hom.: 185 Cov.: 0

Gnomad AFR AF: 0.0284

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0596

Gnomad ASJ AF: 0.00192

Gnomad EAS AF: 0.133

Gnomad SAS AF: 0.0391

Gnomad FIN AF: 0.0304

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00288

Gnomad OTH AF: 0.0174

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.0225 AC: 864 AN: 38426 Hom.: 187 Cov.: 0 AF XY: 0.0239 AC XY: 464 AN XY: 19374

African (AFR) AF: 0.0290 AC: 231 AN: 7966

American (AMR) AF: 0.0601 AC: 206 AN: 3426

Ashkenazi Jewish (ASJ) AF: 0.00192 AC: 2 AN: 1042

East Asian (EAS) AF: 0.132 AC: 216 AN: 1632

South Asian (SAS) AF: 0.0394 AC: 51 AN: 1296

European-Finnish (FIN) AF: 0.0304 AC: 94 AN: 3096

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 48

European-Non Finnish (NFE) AF: 0.00288 AC: 55 AN: 19120

Other (OTH) AF: 0.0170 AC: 9 AN: 528

Alfa AF: 0.0528 Hom.: 23

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	3.8
DANN	Benign	0.58
PhyloP100		0.76
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs2159128; hg19: chr19-950380;